Damage that affects large volumes of skeletal muscle tissue can severely impact health, mobility, and quality-of-life. Efforts to restore muscle function by implanting engineered grafts at the site of damage have demonstrated limited restoration of force production. Various forms of mechanical and biochemical stimulation have been shown to have a potentially beneficial impact on muscle maturation, vascularization, and innervation, but yield unpredictable and inconsistent recovery of functional mobility. Here we show that targeted exercise of optogenetic engineered muscle grafts restores motor functions 2 weeks post-injury. Furthermore, we conduct phosphoproteomic analysis of grafts in vitro and in vivo to show that exercise training alters signaling pathways that play key roles in skeletal muscle contractility, neurite growth, neuromuscular synapse formation, angiogenesis, and cytoskeletal remodeling. Our study uncovers several proteins not previously known to be modulated by exercise, revealing promising mechanisms for leveraging targeted exercise to enhance functional integration of tissue engineered muscle.